{"_id":"chr21:g.36930262A>T","_version":1,"chrom":"21","clingen":{"caid":"CA409910993"},"dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"T","codon_degeneracy":[0,0,0],"codonpos":[1,1,1],"pos":[390,390,390],"ref":"S","refcodon":["TCA","TCA","TCA"]},"alphamissense":{"pred":["B","B"],"rankscore":0.0671,"score":[0.0777,0.0772]},"alt":"T","altai_neandertal":["A","A"],"ancestral_allele":"A","appris":["principal1","principal1","principal1"],"bayesdel":{"add_af":{"pred":"T","rankscore":0.39419,"score":-0.0818219},"no_af":{"pred":"T","rankscore":0.38595,"score":-0.355308}},"bstatistic":{"converted_rankscore":0.20147,"score":917.0},"cadd":{"phred":0.051,"raw_rankscore":0.01118,"raw_score":-0.793902},"chagyrskaya_neandertal":["A","A"],"chrom":"21","clinpred":{"pred":"T","rankscore":0.0307,"score":0.0365094386605547},"dann":{"rankscore":0.00524,"score":0.1765913791204268},"denisova":["A","A"],"deogen2":{"pred":["T","T","T"],"rankscore":0.72375,"score":[0.356973,0.356973,0.356973]},"eigen":{"phred_coding":0.0291729,"raw_coding":-1.7510628110654,"raw_coding_rankscore":0.00676},"eigen-pc":{"phred_coding":0.02591512,"raw_coding":-1.8608243987526,"raw_coding_rankscore":0.00584},"ensembl":{"geneid":["ENSG00000159267","ENSG00000159267","ENSG00000159267"],"proteinid":["ENSP00000479939","ENSP00000338387","ENSP00000382071"],"transcriptid":["ENST00000612277","ENST00000336648","ENST00000399120"]},"esm1b":{"pred":["T","T","T"],"rankscore":0.30096,"score":[-4.44,-4.44,-4.44]},"eve":{"class10_pred":["U","U","U"],"class20_pred":["B","B","B"],"class25_pred":["B","B","B"],"class30_pred":["B","B","B"],"class40_pred":["B","B","B"],"class50_pred":["B","B","B"],"class60_pred":["B","B","B"],"class70_pred":["B","B","B"],"class75_pred":["B","B","B"],"class80_pred":["B","B","B"],"class90_pred":["B","B","B"],"rankscore":0.07068,"score":[0.09859654719859062,0.09859654719859062,0.09859654719859062]},"fathmm":{"converted_rankscore":0.98035,"pred":["D","D"],"score":[-4.71,-4.71]},"fathmm-mkl":{"coding_group":"AEFDBCI","coding_pred":"N","coding_rankscore":0.14399,"coding_score":0.08475},"fathmm-xf":{"coding_pred":"N","coding_rankscore":0.07171,"coding_score":0.044511},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.55848,"score":0.633656},"h1-hesc":{"confidence_value":0,"rankscore":0.55881,"score":0.658983},"huvec":{"confidence_value":0,"rankscore":0.61905,"score":0.655142},"integrated":{"confidence_value":0,"rankscore":0.37627,"score":0.615465}},"gencode_basic":["Y","Y","Y"],"genename":["HLCS","HLCS","HLCS"],"genocanyon":{"rankscore":0.74766,"score":0.999999999319828},"gerp":{"91_mammals":{"rankscore":0.01241,"score":-7.6}},"gerp++":{"nr":5.14,"rs":-10.3,"rs_rankscore":0.00281},"gmvp":{"rankscore":0.48673,"score":0.4875363324645004},"hg18":{"end":37224432,"start":37224432},"hg19":{"end":38302562,"start":38302562},"hg38":{"end":36930262,"start":36930262},"hgvsc":"c.1168T>A","hgvsp":["p.S390T","p.Ser390Thr"],"interpro":{"domain":["Biotin-protein ligase, N-terminal","Biotin-protein ligase, N-terminal","Biotin-protein ligase, N-terminal"]},"list-s2":{"pred":"T","rankscore":0.07184,"score":0.336266},"lrt":{"converted_rankscore":0.10172,"omega":0.860534,"pred":"N","score":0.691441},"m-cap":{"pred":"T","rankscore":0.43768,"score":0.021062},"metalr":{"pred":"D","rankscore":0.87622,"score":0.6453},"metarnn":{"pred":["T","T","T"],"rankscore":0.05653,"score":[0.053898126,0.053898126,0.053898126]},"metasvm":{"pred":"T","rankscore":0.78916,"score":-0.15},"mpc":{"rankscore":0.12603,"score":0.111640583288},"mutationassessor":{"pred":["N","N","N"],"rankscore":0.02835,"score":[-0.44,-0.44,-0.44]},"mutationtaster":{"aae":["S390T","S390T"],"converted_rankscore":0.08975,"model":["simple_aae","simple_aae"],"pred":["N","N"],"score":[1.0,1.0]},"mutformer":{"rankscore":0.80368,"score":0.42949376},"mutpred":{"aa_change":["S390T","S390T","S390T"],"accession":["P50747","P50747","P50747"],"pred":[{"mechanism":"Loss of catalytic residue at L386","p_val":0.2146},{"mechanism":"Loss of catalytic residue at L386","p_val":0.2146},{"mechanism":"Loss of catalytic residue at L386","p_val":0.2146}],"rankscore":0.70733,"score":[0.581,0.581,0.581]},"mvp":{"rankscore":0.67332,"score":[0.676068496136,0.676068496136,0.676068496136]},"phactboost":{"rankscore":0.08484,"score":[0.000783658027152726,0.000783658027152726,0.000783658027152726]},"phastcons":{"100way_vertebrate":{"rankscore":0.06391,"score":0.0},"17way_primate":{"rankscore":0.1937,"score":0.125},"470way_mammalian":{"rankscore":0.08366,"score":0.0}},"phylop":{"100way_vertebrate":{"rankscore":0.05386,"score":-0.665},"17way_primate":{"rankscore":0.11795,"score":-0.156},"470way_mammalian":{"rankscore":0.06726,"score":-0.977}},"polyphen2":{"hdiv":{"pred":["B","B","B"],"rankscore":0.07471,"score":[0.001,0.001,0.001]},"hvar":{"pred":["B","B","B"],"rankscore":0.04355,"score":[0.001,0.001,0.001]}},"primateai":{"pred":"T","rankscore":0.02856,"score":0.24072688818},"provean":{"converted_rankscore":0.03761,"pred":["N","N"],"score":[0.35,0.35]},"ref":"A","reliability_index":10,"revel":{"rankscore":0.46613,"score":[0.189,0.189]},"sift":{"converted_rankscore":0.00964,"pred":["T","T"],"score":[1.0,1.0]},"sift4g":{"converted_rankscore":0.01155,"pred":["T","T","T"],"score":[1.0,1.0,1.0]},"siphy_29way":{"logodds_rankscore":0.03162,"logodds_score":1.9507,"pi":{"a":0.1831,"c":0.152,"g":0.3455,"t":0.3194}},"tsl":[5,1,1],"uniprot":[{"acc":"P50747","entry":"BPL1_HUMAN"},{"acc":"P50747","entry":"BPL1_HUMAN"},{"acc":"P50747","entry":"BPL1_HUMAN"}],"varity":{"er":{"rankscore":0.02268,"score":[0.03354722,0.03354722,0.03354722]},"er_loo":{"rankscore":0.02268,"score":[0.03354722,0.03354722,0.03354722]},"r":{"rankscore":0.087,"score":[0.049208794,0.049208794,0.049208794]},"r_loo":{"rankscore":0.08699,"score":[0.049208794,0.049208794,0.049208794]}},"vep_canonical":"YES","vest4":{"rankscore":0.07125,"score":[0.089,0.092,0.089]},"vindijia_neandertal":["A","A"]},"hg38":{"end":36930262,"start":36930262},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"6019","position":"1648"},"cds":{"length":"2181","position":"1168"},"effect":"missense_variant","feature_id":"NM_000411.6","feature_type":"transcript","gene_id":"HLCS","genename":"HLCS","hgvs_c":"c.1168T>A","hgvs_p":"p.Ser390Thr","protein":{"length":"726","position":"390"},"putative_impact":"MODERATE","rank":"6","total":"12","transcript_biotype":"protein_coding"},{"cdna":{"length":"6953","position":"2582"},"cds":{"length":"2181","position":"1168"},"effect":"missense_variant","feature_id":"NM_001242784.1","feature_type":"transcript","gene_id":"HLCS","genename":"HLCS","hgvs_c":"c.1168T>A","hgvs_p":"p.Ser390Thr","protein":{"length":"726","position":"390"},"putative_impact":"MODERATE","rank":"6","total":"12","transcript_biotype":"protein_coding"},{"cdna":{"length":"6112","position":"1741"},"cds":{"length":"2181","position":"1168"},"effect":"missense_variant","feature_id":"NM_001242785.1","feature_type":"transcript","gene_id":"HLCS","genename":"HLCS","hgvs_c":"c.1168T>A","hgvs_p":"p.Ser390Thr","protein":{"length":"726","position":"390"},"putative_impact":"MODERATE","rank":"6","total":"12","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"T","position":"36930262","ref":"A"}}